SERVER WONT UPDATE!!!

When updating from 1.5.2 to 1.6.2, my server start.command (terminal on mac osx version 10.6.8) has not been updated and still starts the 1.5.2 server. to start up the 1.6.2 server, i need to open it using a jar which is a bit of pain. furthermore, now the jar loads up the server as usual but when u go to join the server it says cant connect to server so i cant play at all now. any help is much appreciated, thanks.